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cellxgene-census

80 / 100 · Low risk

Fine to try.

By KalarisLabs/research-agent-skills (GitHub) · research · 126 stars · scanned at commit 802bbea

Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell metadata, gene expression slices, Census summary counts, source H5AD URIs/downloads, embeddings, spatial Census data, or reference atlas comparisons across organisms, tissues, diseases, assays, and cell types. For analyzing your own local single-cell data use scanpy, anndata, or scvi-tools.

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'cellxgene-census' ] || [ -L ~/.agents/skills/'cellxgene-census' ]; then echo 'A skill folder named cellxgene-census already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/KalarisLabs/research-agent-skills' "$d" && git -C "$d" checkout --quiet '802bbea44e551abac24d6856f83fc55149bbdba3' -- 'skills/cellxgene-census' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/cellxgene-census' ~/.agents/skills/'cellxgene-census' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'cellxgene-census' ~/.claude/skills/'cellxgene-census' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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